Team Rocket: Under New Management
by Kamen Rider Olympus
Summary: Anti-villain Naruto, Naruharem. Found by Giovanni as a baby, Naruto rose through the ranks of Team Rocket. But after Giovanni disappears and Naruto's brother betrays Team Rocket, only one man is left to become the new Boss of Team Rocket. And he isn't going to take failure as an option anymore. Expand Team Rocket, beat the other teams, conquer the world. These are his only motives.


**Sup? I'm Olympus and this is my first fic on this site.**

**It's a reincarnation!Naruto story of Naruto being born in the Pokemon world. The twist? Abandoned as a baby, he was found by Giovanni and eventually grew up to be a member of Team Rocket up until it's disbandment in G/S/C/HG/SS. Instead of it disbanding, Naruto has become the new Boss. However, with goody-good trainers, gym leaders, the elite four of all the regions, and an inter-team war among Team Rocket, Magma, Aqua, Galactic, Plasma, and Flare on the way, it'll be a wild ride.**

**This is a mix of anime, manga, and game canon, but mostly the game canon.**

**Disclaimer: I do not own Pokemon or Naruto.**

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><p><strong>Chapter 1: The Son of the Boss<strong>

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><p>"I gave birth to this demon spawn and cannot stand even looking at his face. As the gym leader of Viridian City, please take this child off my hands and to the Officer Jenny in Vermillion City.<p>

Tell her to take him. His name is Naruto."

A baby was left at the door of Viridian City's gym. The gym leader, Giovanni, stared at the letter and down at the baby.

Take it to Vermillion City? To the justice system? No. He wanted nothing to do with that.

"Demon spawn, hm?" The gym leader mused, peering down at the sleeping baby. To his surprise, whiskers seemed to grow from the child's cheeks.

The baby woke, and peered up at the gym leader. The gym leader stared back.

"You know," Giovanni pondered aloud, "My mother- I mean, Madame Boss, would love to have you around, Naruto."

It was then that Naruto was inducted into Giovanni's mafia family.

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><p>Naruto was three years old when his younger brother was born. His family was already strange emough. Madame Boss, his grandmother, was strict with everyone except for Naruto. Giovanni was unwed and as such, when he returned from heists for Team Rocket, spent time introducing Naruto to Pokemon.<p>

He wouldn't learn until much later, but Naruto's younger brother was born from a one-night stand with another member of Team Rocket, Ariana. Giovanni and Ariana didn't want to speak about it, but wanted Naruto and the new baby to live life as brothers.

"Naruto."

The young, blonde toddler looked up from his blocks and over at his father.

"Come meet your baby brother. Silver."

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><p>Naruto and Silver were as different as daylight and dark.<p>

Silver was a serious soul with a no nonsense point of view. He was considered the "smarter" of the duo; cold and calculating in everything he did. However, he had a fierce temper to match his fiery red hair and could be really brash at times.

Conversely, Naruto was a loudmouthed, outgoing soul. While Team Rocket admins preferred Silver, the grunts all loved Naruto. While he seemed a little dim, he would coach grunts on how to use Pokemon on the side, even though he didn't have a Pokemon of his own yet. This made Giovanni name Naruto as his favorite.

This wasn't the happiest of news to Silver.

Thus began a modern day Cain and Abel story.

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><p>Madame Boss' funeral was not celebrated. A few moments of silence and they moved on. She was killed from Mewtwo's, a clone of the legendary Mew, destruction of a lab and consequential escape.<p>

"Naruto."

The young boy looked up at his father, rubbing at his eyes to try and hide his tears, "What?"

Giovanni didn't say a word. He placed a Pokeball in Naruto's hands and walked off. Now that Giovanni was the new leader of Team Rocket, he had a lot to tend to. Naruto gazed down at his Pokeball, before pressing a button in the middle, releasing the Pokemon inside.

"Larvitar!"

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><p>Gas flooded the Pokemon Tower, knocking out the mediums and their Pokemon inside. Mr. Fuji covered his mouth with his hand wheezed, "You'll never get away with-" it was then that the gas finally affected him, causing him to be knocked out as well.<p>

"Good job, Naruto!" A fellow Team Rocket Grunt in a gas mask congratulated him.

Adjusting the black cap on his head, the blonde chuckled behind his own gas mask, "Was nothing."

"Modest, too!" Another Rocket grunt added, "One of these days, you'll be our new boss, I can feel it!"

Naruto just rubbed the back of his neck and grinned under his mask as the gas cleared. Ever since he had become a Team Rocket Grunt, he had been known as the strongest Grunt, mostly for using tactics that other grunts hadn't ever thought about using. Just with his partner, Larvitar.

"..."

"Who's that kid?" A Grunt asked, in confusion.

"Not just that," another Grunt asked, stepping forward, "why ain't he sayin' nothin'?"

Naruto's eyes widened, as he stepped forward and asked, "You... You're the kid who defeated Dad in Celadon City, aren't you?"

The boy, with a Charizard by his side, said nothing.

Naruto scowled before releasing his Larvitar onto the floor and ordering, "Larvitar, Rock Slide!"

The green reptilian Pokemon nodded in affirmation before summoning a storm of rocks and crashing it towards its opponent. To Naruto's surprise, Red did nothing but mutter something quietly to its Charizard. The nails of the beast began to glow as it rushed towards the rocks, destroying them by using Metal Claw.

It didn't stop there.

Its claws slashed into Naruto's Larvitar, sending it barreling backwards and crashing into Naruto, knocking them both over.

A one hit KO.

The undefeatable Pokemon Grunt was defeated by a silent boy named Red. He watched in horror as the Grunts released the gas again, only for the Charizard to blow it away with its wings.

They lost.

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><p>"Team Rocket is disbanded." Those were the last words Naruto heard, over his bootleg Pokegear, from his father. Giovanni had lost to Red three times, and this last time was the final straw. Giovanni wanted to become stronger, but to do that, he would have to leave Team Rocket behind.<p>

"Good riddance."

Naruto clenched his fists and decked Silver in the face for saying that, exclaiming, "Where the hell do you get off?! That's our father, you're talking about!"

Silver glared back up at his older brother and snapped, "OUR father?! No! I'M his son! Not you!"

Staggering up to his feet, he continued, "You're just some abandoned baby he found in Viridian City! Well?! What do you think about that?!"

Naruto clenched his fists. Giovanni had already told him this. Yes, it hurt. Yes, he wished he was actually Giovanni's son by birth. But at this point, it didn't matter. Their father abandoned Team Rocket. He abandoned _them._

_"_Can't say anything, huh?" Silver spat, turning around and beginning to make his way out of Team Rocket's underground base.

"Where are you going?!" Naruto demanded, about ready to clobber his younger brother again.

Silver stopped, but didn't turn around to face Naruto. Instead, he asked a question:

"Is this the end of Team Rocket?"

"Of course it isn't!"

Naruto turned to see that the four executives of Team Rocket: Archer, Ariana, Petrel, and Proton, stood beside him to confront Silver.

"This isn't the end!" the cyan haired Archer repeated, "We'll reform Team Rocket! And we'll bring the Boss back to us as well!"

"And until then?" Silver asked with a frown, "What will you do?"

"Heheheh," the devious and pink haired man named Petrel chimed in, "We'll just reinstate his only remaining child as the Boss!"

Silver's mocking sneer turned into an angry one. Ariana's eyes darted from Naruto to Silver and back again. Naruto simply said nothing.

"Then I'll just do what Red did and crush my bro- no," Silver shook his head, "Naruto, myself."

Once again, Silver turned to walk away, only to be stopped by his mother Ariana's call, "Silver, wait!"

Silver was still and quiet for a moment before stating, "Goodbye, mother."

From that day on, Silver was one of Team Rocket's sworn enemies.

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><p>It had been three years since Naruto had seen Silver, and three years since he turned down Team Rocket's offer to become the new Boss. Now at eighteen, he had become the newest member of the Team Rocket Executives while Archer became the interim Boss of Team Rocket.<p>

Yet here Naruto was, staring down his fifteen year old brother in the Goldenrod Radio Tower. He knew why he was there. He wanted to stop the radio broadcasts and officially take down Team Rocket once and for all.

And Naruto wasn't willing to help him do that.

"So, you're the new boss, huh?" Silver asked, his voice laced with venom.

"That's funny," Naruto grinned mischievously, "I coulda sworn that Archer was our acting leader."

"Stow it," the red haired teen shook his head, "We both know that I defeated Archer and that you could beat his ass from here to Unova."

"Heheheh," the whiskered Rocket member chuckled, "True."

Silver smirked, "Then, this is it. The end of Team Rocket is now. Prepare yourself." Silver reached into his black hoodie pocket and pulled out a Pokeball.

Unclipping a Pokeball from his white Team Rocket uniform, Naruto just laughed and replied, "You're about to be sadly mistaken. Sorry. Oh, wait. I ain't sorry in the least."

Gritting his teeth in anger, Silver threw the Pokeball, "Feraligatr, the time has come!"

A large blue alligator burst forth before the two boys. With a hefty roar, it declared its name, "Feraaaaligatr!"

Naruto sized up the Pokemon once. A fully evolved starter Pokemon. The Pokemon given to Rocket Grunts and Executives such as Koffing, Zubat, and Rattata wouldn't be enough for sure. He knew who he had to rely on.

"Pupitar, for the glory of Rocket!"

A blue rock cocoon emerged from its Pokeball, but said nothing.

Silver scoffed, as a smirk spread across his lips, "A Rock/Ground type, huh? That might be your first 'Mon, but it'll be your downfall against a Water Type. Feraligatr, Ice Fang!"

A cold breath began to emanate from the alligator. It lunged forward, it's fangs becoming encased in ice, ready to crunch into the pupa Pokemon.

"Let's put Double Team on repeat, Pupitar!" Naruto commanded.

It was then that Pupitar began to multiply and surround Feraligatr. Silver was about to order to cancel the attack, but it was too late. The water type lunged, but hit one of the copies and landed on the floor of the Radio Tower.

"Now, poison it!" The Rocket Executive ordered.

While Feraligatr was getting back up, the real Pupitar shot a jet of poison at the opponent, also known as the move Toxic. Splashing the creature in the back, the reptilian Pokemon gave a roar in pain.

"Hit it with Surf!"

Naruto's grin broadened, "You just fucked up."

"What?!" Silver couldn't believe that. All Surf would have to do is hit Pupitar once and it would go down instantly. There was no way Naruto could have won this match.

When Naruto yelled his next command, that was when Silver finally realized something.

Giovanni had bred Pupitar especially for Naruto. Naruto was their father's favorite son.

"Dragon Dance!"

A move Pupitar could only know if it was bred with an Axew. Incorporating a jump with its funky rhythm, the Pupitar barely dodged the large wave Feraligatr had summoned.

"Rock Slide!"

Stronger and more powerful than usual, a storm of rocks flooded towards Feraligatr. Pelting it with every single hit of the debris, the large reptile was flung backwards and into Silver, unable to do battle. The now pained red head could do nothing more but return Feraligatr to its Pokeball.

"Naruto..." Silver growled, "You haven't won... I still have five more Pokemon to battle with!"

No. Naruto had won and Silver knew it. Pupitar's evasiveness was at an all-time high and Naruto would most likely use Dragon Dance again and again to make Pupitar stronger and faster with each passing moment.

Cain had bested Abel; older brother had defeated his younger brother.

"Silver!" A boy in a gold hat exclaimed, "You okay?!"

"Damn you, Ethan..." Silver growled, glaring at his rival, "I told you to get lost! Defeating Team Rocket is my burden and my burden alone!"

"You seem to be doing a shitty job at it, you know," Naruto couldn't help but snark.

Ethan laughed and agreed with the Rocket Executive, "Man, has he got you pegged. Oh, well. Guess I'll take this guy out."

"I'd love to see you try, squirt," the blonde criminal offered with a smirk.

"This is my batt-" But to Silver's dismay, Ethan had already thrown out a Pokemon.

Out in front of the boy was a blue beetle, "Heracross!"

"Huh," Naruto mused, "You may have a type advantage, but so did Silver. This will end really easily, I can bet my entire pantry full of ramen on that."

"Oh, really?" Ethan asked, as he rolled his shirt sleeve up, exposing a strange bracelet.

Naruto's eyes widened. He had heard about this. Could that be a...

"Mega Ring, activate!"

A flash of light exuded from the bracelet and consumed Heracross. When it finally faded, pink accents had been added to the creature and it's horn was changed to a thicker design.

"So this is Mega Evolution, huh?" Naruto asked, before grinning, "Now this might be an actual challenge."

"No it won't," Ethan shook his head and grinned as well, "Just watch and see."

"Geez, you're a stubborn kid; but so am I," Naruto exclaimed, "Rock Slide, Pupitar!"

"Brick Break!"

Time seemed to slow to a standstill for Naruto. Something about this was too familiar. The rocks flew towards Mega Heracross, but the beetle swiped them away easily. With great speed and precision, the Heracross slammed Pupitar into the ground, causing both Pokemon to fall through to the floors below.

For once in Naruto's life, his knees began to grow weak.

This was the second loss he had suffered in his career as a member of Team Rocket.

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><p>"Are you sure you want to do this, Naruto?" Ariana asked, as Naruto had called an assembly in Team Rocket's new underground base in Johto.<p>

"Yeah," the blonde boy nodded, "Damn sure." This was going to be Team Rocket's turning point. No. This was going to be his own turning point.

He stepped out on the makeshift stage and scanned the crowd. Lots of Team Rocket members had abandoned the gang after this last loss. In fact, Naruto could name all of the people who were still there.

Of course, the four other executives were still there, even though Archer wanted to disband Team Rocket like Giovanni did. Three bumbling grunts, known as Jessie, James, and Meowth, had unfortunately decided to stick around too. Other notable members were Butch and Cassidy, Atilla and Hun, Annie and Oakley, Domino, and an elite trio of Team a Rocket members known as the Three Beasts. Not a terrible turn out but not a great one either.

"Dear members of Team Rocket," Naruto began to make his speech, "Today is the day that we end our streak of losing. As you all may know, we aren't the only team bent on extending our reach to the stars above. No. Team Aqua and Magma. Team Galactic. Team Plasma. Team Flare. They all want to do the same thing."

"What's dat gotta do with us?" The talking Meowth asked, crossing his furry arms.

"Yeah, we don't even have a leader!" Jessie added, to Archer's dismay and annoyance.

"Yes, you do," a grin crept across Naruto's lips. A smile crossed Ariana, Proton, and Petrel's lips as well while Archer began to frown deeper.

"I'm going to be the new Boss of Team Rocket. There's going to be some changes around here.'

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><p><strong>And there's the first chapter. What did you think? Let me know!<strong>

**Question time! These two questions will help formulate some upcoming plot points in this story!**

**1. What Pokemon do you want to see Naruto catch/steal for his team?**

**2. What girls do you want to see joining Naruto's harem? They can be any girl from Pokemon canon and you can name up to five for suggestion!**

**Until next time!**


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